We have found a method to prepare polynucleotides so that they can be visualized in the Scanning Tunneling Microscope (STM). We want to study this system in an effort to examine its utility in an STM-based system for sequencing DNA. 2'-deoxynucleoside 5'-O-(1-thiotriphosphates) are substrates for the Thermus aquaticus DNA polymerase under the conditions of the polymerase chain reaction. Sulfur atoms in the resulting polynucleotides are located on the internucleotide phosphodiester groupings. This anionic sulfur binds divalent mercury in the form of 4- hydroxymercuribenzoate, a complex which is visible in STM. DNA sequence determinations have become one of the most important tools now available in biochemistry and molecular biology. The availability of such sequences is important in many different areas, including the study of infectious and hereditary disease as well as in the study of human ontogeny and molecular and organismic phylogeny.